PDXJ_ECOLI
ID PDXJ_ECOLI Reviewed; 243 AA.
AC P0A794; P24223; Q2MAG6;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Pyridoxine 5'-phosphate synthase;
DE Short=PNP synthase;
DE EC=2.6.99.2 {ECO:0000269|PubMed:10225425};
GN Name=pdxJ; OrderedLocusNames=b2564, JW2548;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=K12;
RX PubMed=1537799; DOI=10.1128/jb.174.5.1544-1553.1992;
RA Takiff H.E., Baker T., Copeland T., Chen S.-M., Court D.L.;
RT "Locating essential Escherichia coli genes by using mini-Tn10 transposons:
RT the pdxJ operon.";
RL J. Bacteriol. 174:1544-1553(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1537800; DOI=10.1128/jb.174.5.1554-1567.1992;
RA Lam H.-M., Tancula E., Dempsey W.B., Winkler M.E.;
RT "Suppression of insertions in the complex pdxJ operon of Escherichia coli
RT K-12 by lon and other mutations.";
RL J. Bacteriol. 174:1554-1567(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Nashimoto H., Saito N.;
RL Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP VARIANT SER-194.
RX PubMed=8636054; DOI=10.1128/jb.178.8.2445-2449.1996;
RA Man T.K., Zhao G., Winkler M.E.;
RT "Isolation of a pdxJ point mutation that bypasses the requirement for the
RT PdxH oxidase in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia
RT coli K-12.";
RL J. Bacteriol. 178:2445-2449(1996).
RN [7]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=K12 / ATCC 35607 / JM83;
RX PubMed=10225425; DOI=10.1016/s0014-5793(99)00393-2;
RA Laber B., Maurer W., Scharf S., Stepusin K., Schmidt F.S.;
RT "Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-
RT (phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and
RT PdxJ protein.";
RL FEBS Lett. 449:45-48(1999).
RN [8]
RP CRYSTALLIZATION.
RX PubMed=10944349; DOI=10.1107/s0907444900007368;
RA Garrido Franco M., Huber R., Schmidt F.S., Laber B., Clausen T.;
RT "Crystallization and preliminary X-ray crystallographic analysis of PdxJ,
RT the pyridoxine 5'-phosphate synthesizing enzyme.";
RL Acta Crystallogr. D 56:1045-1048(2000).
RN [9]
RP REVIEW.
RX PubMed=12686115; DOI=10.1016/s1570-9639(03)00065-7;
RA Garrido-Franco M.;
RT "Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and
RT beyond.";
RL Biochim. Biophys. Acta 1647:92-97(2003).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH PRODUCT, AND SUBUNIT.
RX PubMed=11286891; DOI=10.1016/s0969-2126(01)00584-6;
RA Garrido Franco M., Laber B., Huber R., Clausen T.;
RT "Structural basis for the function of pyridoxine 5'-phosphate synthase.";
RL Structure 9:245-253(2001).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF APOENZYME AND COMPLEX WITH
RP SUBSTRATE, AND SUBUNIT.
RX PubMed=12269807; DOI=10.1021/bi026292t;
RA Yeh J.I., Du S., Pohl E., Cane D.E.;
RT "Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal
RT structure in complex with 1-deoxy-D-xylulose phosphate.";
RL Biochemistry 41:11649-11657(2002).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE AND
RP SUBSTRATE ANALOG, AND REACTION MECHANISM.
RX PubMed=12206776; DOI=10.1016/s0022-2836(02)00695-2;
RA Garrido-Franco M., Laber B., Huber R., Clausen T.;
RT "Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications
RT for substrate binding and catalysis.";
RL J. Mol. Biol. 321:601-612(2002).
CC -!- FUNCTION: Catalyzes the complicated ring closure reaction between the
CC two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-
CC 2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form
CC pyridoxine 5'-phosphate (PNP) and inorganic phosphate.
CC {ECO:0000269|PubMed:10225425}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate
CC = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate;
CC Xref=Rhea:RHEA:15265, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57279, ChEBI:CHEBI:57792,
CC ChEBI:CHEBI:58589; EC=2.6.99.2;
CC Evidence={ECO:0000269|PubMed:10225425};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis;
CC pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5.
CC {ECO:0000269|PubMed:10225425}.
CC -!- SUBUNIT: Homooctamer; tetramer of dimers. {ECO:0000269|PubMed:11286891,
CC ECO:0000269|PubMed:12269807}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the PNP synthase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=D64044; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; M76470; AAA21845.1; -; Genomic_DNA.
DR EMBL; M74526; AAA24315.1; -; Genomic_DNA.
DR EMBL; D64044; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U36841; AAA79826.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75617.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76740.1; -; Genomic_DNA.
DR PIR; A42293; A42293.
DR RefSeq; NP_417059.1; NC_000913.3.
DR RefSeq; WP_001297412.1; NZ_STEB01000011.1.
DR PDB; 1HO1; X-ray; 2.00 A; A/B/C/D=2-243.
DR PDB; 1HO4; X-ray; 2.30 A; A/B/C/D=2-243.
DR PDB; 1IXN; X-ray; 2.30 A; A/B/C/D=2-243.
DR PDB; 1IXO; X-ray; 2.30 A; A/B/C/D=2-243.
DR PDB; 1IXP; X-ray; 2.30 A; A/B/C/D=2-243.
DR PDB; 1IXQ; X-ray; 2.30 A; A/B/C/D=2-243.
DR PDB; 1M5W; X-ray; 1.96 A; A/B/C/D/E/F/G/H=1-243.
DR PDB; 6RG0; X-ray; 3.07 A; A/B/C/D=2-243.
DR PDBsum; 1HO1; -.
DR PDBsum; 1HO4; -.
DR PDBsum; 1IXN; -.
DR PDBsum; 1IXO; -.
DR PDBsum; 1IXP; -.
DR PDBsum; 1IXQ; -.
DR PDBsum; 1M5W; -.
DR PDBsum; 6RG0; -.
DR AlphaFoldDB; P0A794; -.
DR SMR; P0A794; -.
DR BioGRID; 4260601; 32.
DR DIP; DIP-36215N; -.
DR IntAct; P0A794; 5.
DR STRING; 511145.b2564; -.
DR DrugBank; DB02496; 1-Deoxy-D-xylulose 5-phosphate.
DR DrugBank; DB02209; Pyridoxine phosphate.
DR DrugBank; DB02515; sn-glycerol 3-phosphate.
DR jPOST; P0A794; -.
DR PaxDb; P0A794; -.
DR PRIDE; P0A794; -.
DR EnsemblBacteria; AAC75617; AAC75617; b2564.
DR EnsemblBacteria; BAE76740; BAE76740; BAE76740.
DR GeneID; 66673547; -.
DR GeneID; 947039; -.
DR KEGG; ecj:JW2548; -.
DR KEGG; eco:b2564; -.
DR PATRIC; fig|1411691.4.peg.4170; -.
DR EchoBASE; EB0687; -.
DR eggNOG; COG0854; Bacteria.
DR HOGENOM; CLU_074563_0_0_6; -.
DR InParanoid; P0A794; -.
DR OMA; SNAGWDT; -.
DR PhylomeDB; P0A794; -.
DR BioCyc; EcoCyc:PDXJ-MON; -.
DR BioCyc; MetaCyc:PDXJ-MON; -.
DR BRENDA; 2.6.99.2; 2026.
DR UniPathway; UPA00244; UER00313.
DR EvolutionaryTrace; P0A794; -.
DR PRO; PR:P0A794; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0033856; F:pyridoxine 5'-phosphate synthase activity; IDA:EcoCyc.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:EcoliWiki.
DR CDD; cd00003; PNPsynthase; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00279; PdxJ; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR004569; PyrdxlP_synth_PdxJ.
DR InterPro; IPR036130; Pyridoxine-5'_phos_synth.
DR PANTHER; PTHR30456; PTHR30456; 1.
DR Pfam; PF03740; PdxJ; 1.
DR SUPFAM; SSF63892; SSF63892; 1.
DR TIGRFAMs; TIGR00559; pdxJ; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing;
KW Pyridoxine biosynthesis; Reference proteome; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..243
FT /note="Pyridoxine 5'-phosphate synthase"
FT /id="PRO_0000190114"
FT ACT_SITE 45
FT /note="Proton acceptor"
FT ACT_SITE 72
FT /note="Proton acceptor"
FT ACT_SITE 193
FT /note="Proton donor"
FT BINDING 9
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT BINDING 11..12
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT BINDING 20
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT BINDING 47
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT BINDING 52
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT BINDING 102
FT /ligand="1-deoxy-D-xylulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:57792"
FT BINDING 194
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT BINDING 215..216
FT /ligand="3-amino-2-oxopropyl phosphate"
FT /ligand_id="ChEBI:CHEBI:57279"
FT SITE 153
FT /note="Transition state stabilizer"
FT VARIANT 194
FT /note="G -> S (in pdxH null mutation suppressor)"
FT /evidence="ECO:0000269|PubMed:8636054"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 11..18
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 20..22
FT /evidence="ECO:0007829|PDB:1HO4"
FT HELIX 27..35
FT /evidence="ECO:0007829|PDB:1M5W"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 40..45
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 55..64
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 66..73
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 77..86
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 89..93
FT /evidence="ECO:0007829|PDB:1M5W"
FT TURN 98..100
FT /evidence="ECO:0007829|PDB:1HO1"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:1IXP"
FT HELIX 110..112
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 113..125
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 129..134
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 138..146
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 150..155
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 157..161
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 165..184
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:1M5W"
FT TURN 197..199
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 200..204
FT /evidence="ECO:0007829|PDB:1M5W"
FT STRAND 209..214
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 216..225
FT /evidence="ECO:0007829|PDB:1M5W"
FT HELIX 227..242
FT /evidence="ECO:0007829|PDB:1M5W"
SQ SEQUENCE 243 AA; 26384 MW; BF513A5B844E8CB2 CRC64;
MAELLLGVNI DHIATLRNAR GTAYPDPVQA AFIAEQAGAD GITVHLREDR RHITDRDVRI
LRQTLDTRMN LEMAVTEEML AIAVETKPHF CCLVPEKRQE VTTEGGLDVA GQRDKMRDAC
KRLADAGIQV SLFIDADEEQ IKAAAEVGAP FIEIHTGCYA DAKTDAEQAQ ELARIAKAAT
FAASLGLKVN AGHGLTYHNV KAIAAIPEMH ELNIGHAIIG RAVMTGLKDA VAEMKRLMLE
ARG
